Cutaneous wounds are major contributors to patient mortality, healthcare costs, and impairedquality of life. Instead of progressing through the normal stages of skin repair, chronic wounds fail to heal. Upon a break in the skin barrier, wounds are colonized by microbes from our surrounding skin flora, other body sites, and environment. In this body of work, we explore how genetic variability in the bacteria colonizing wounds drives their clinical outcomes. Chapters 2-3 focus on diabetic foot ulcers (DFU), a prevalent type of chronic wound with high rates of infection, lower extremity amputation, and death. Staphylococcus aureus is among the most prevalent and abundant microbial species in DFU, and we previously showed that the effects of S. aureus colonization on DFU healing vary between different strains within the species. In Chapter 2, we performed high-throughput phenotyping assays for virulence on 220 isolates of S. aureus from 60 DFU and found that strains producing higher levels of the golden antioxidant pigment staphyloxanthin survived exposure to neutrophil-mediated oxidative stress and impaired diabetic wound healing in an in vivo diabetic wounding model. Our genomic and transcriptomic analyses implicated transcription factor Sigma B in contributing to variable staphyloxanthin production between strains but suggested that its function may be convergently lost as nonhealing DFU transition from early-stage inflammation to persistent stalled healing. In Chapter 4, we analyzed the phylogenetic, pan-genome, and sequencelevel diversity of 220 whole Staphylococcus aureus genomes cultured and sequenced from DFU, comparing their genetic variation within and between individual DFU in the context of clinical outcomes and the in vitro virulence phenotypes. We characterized the role of the Sigma B-dependent operon yabJ-spoVG in modulating staphyloxanthin production and other virulence activity in S. aureus. In Chapter 5, we examined the bacterial community composition of 406 acute and chronic wounds and identified relationships between wound microbiota and care practices, inflammation, and patient-reported pain. These results provide potential biomarkers and therapeutic targets in the wound microbiome for adverse outcomes in wound healing.